This paper compares the effects of different physics lists on the dose of proton boron capture therapy (PBCT) in Monte Carlo Geant4 simulation. Geant4 was used to establish PBCT model with three different physics lists (FTFP, QBBC and QGSP). Comparison is made for dose distribution of three physics lists with and without boron using an 80 MeV proton beam, as well as the nuclear reaction product data of a 3 MeV proton beam bombarding pure boron. There is no significant difference in the dose distribution of the three physics lists in the water phantom with and without boron, and the consistency of different physics models’ percentage depth dose (PDD) curves is good. The PBCT nuclear reaction products obtained from FTFP physics list are significantly less than those obtained from QBBC and QGSP physics lists. The yields, mean energies and energy ranges of the alpha particles obtained from the QGSP physics list are more consistent with the actual situation than that of the QBBC physics list. The QGSP physics list in Geant4 is more suitable for MC simulation studies of PBCT, judging by a comprehensive evaluation of the inelastic scattering models used by the three physics lists and the simulated nuclear reaction data.